From 9823317e8fe51dba7edf2c583f002f8f6cb45037 Mon Sep 17 00:00:00 2001
From: Heng Li <lh3@me.com>
Date: Wed, 5 Jul 2017 18:23:50 -0400
Subject: [PATCH] r158: optionally ignore base quality

---
 main.c     | 6 ++++--
 map.c      | 3 ++-
 minimap.h  | 1 +
 minimap2.1 | 5 ++++-
 4 files changed, 11 insertions(+), 4 deletions(-)

diff --git a/main.c b/main.c
index 6b15266..153f408 100644
--- a/main.c
+++ b/main.c
@@ -10,7 +10,7 @@
 #include "minimap.h"
 #include "mmpriv.h"
 
-#define MM_VERSION "2.0-r153-pre"
+#define MM_VERSION "2.0-r158-pre"
 
 void liftrlimit()
 {
@@ -70,7 +70,7 @@ int main(int argc, char *argv[])
 	mm_realtime0 = realtime();
 	mm_mapopt_init(&opt);
 
-	while ((c = getopt_long(argc, argv, "aw:k:t:r:f:Vv:g:I:d:XT:s:x:Hcp:M:n:z:A:B:O:E:m:D:N:", long_options, &long_idx)) >= 0) {
+	while ((c = getopt_long(argc, argv, "aw:k:t:r:f:Vv:g:I:d:XT:s:x:Hcp:M:n:z:A:B:O:E:m:D:N:Q", long_options, &long_idx)) >= 0) {
 		if (c == 'w') w = atoi(optarg);
 		else if (c == 'k') k = atoi(optarg);
 		else if (c == 'H') is_hpc = 1;
@@ -87,6 +87,7 @@ int main(int argc, char *argv[])
 		else if (c == 'c') opt.flag |= MM_F_CIGAR;
 		else if (c == 'X') opt.flag |= MM_F_AVA | MM_F_NO_SELF;
 		else if (c == 'a') opt.flag |= MM_F_OUT_SAM | MM_F_CIGAR;
+		else if (c == 'Q') opt.flag |= MM_F_NO_QUAL;
 		else if (c == 'T') opt.sdust_thres = atoi(optarg);
 		else if (c == 'n') opt.min_cnt = atoi(optarg);
 		else if (c == 'm') opt.min_chain_score = atoi(optarg);
@@ -161,6 +162,7 @@ int main(int argc, char *argv[])
 		fprintf(stderr, "    -z INT     Z-drop score [%d]\n", opt.zdrop);
 		fprintf(stderr, "    -s INT     minimal peak DP alignment score [%d]\n", opt.min_dp_max);
 		fprintf(stderr, "  Input/Output:\n");
+		fprintf(stderr, "    -Q         ignore base quality in the input\n");
 		fprintf(stderr, "    -a         output in the SAM format (PAF by default)\n");
 		fprintf(stderr, "    -c         output CIGAR in PAF\n");
 		fprintf(stderr, "    -t INT     number of threads [%d]\n", n_threads);
diff --git a/map.c b/map.c
index 1b2f1d1..2c4a220 100644
--- a/map.c
+++ b/map.c
@@ -305,9 +305,10 @@ static void *worker_pipeline(void *shared, int step, void *in)
 	int i, j;
     pipeline_t *p = (pipeline_t*)shared;
     if (step == 0) { // step 0: read sequences
+		int with_qual = (!!(p->opt->flag & MM_F_OUT_SAM) && !(p->opt->flag & MM_F_NO_QUAL));
         step_t *s;
         s = (step_t*)calloc(1, sizeof(step_t));
-		s->seq = bseq_read(p->fp, p->mini_batch_size, !!(p->opt->flag & MM_F_OUT_SAM), &s->n_seq);
+		s->seq = bseq_read(p->fp, p->mini_batch_size, with_qual, &s->n_seq);
 		if (s->seq) {
 			s->p = p;
 			for (i = 0; i < s->n_seq; ++i)
diff --git a/minimap.h b/minimap.h
index fc3f4fc..ef3d713 100644
--- a/minimap.h
+++ b/minimap.h
@@ -11,6 +11,7 @@
 #define MM_F_AVA       0x02
 #define MM_F_CIGAR     0x04
 #define MM_F_OUT_SAM   0x08
+#define MM_F_NO_QUAL   0x10
 
 #define MM_IDX_MAGIC   "MMI\2"
 
diff --git a/minimap2.1 b/minimap2.1
index ee6c3e0..2f81a1d 100644
--- a/minimap2.1
+++ b/minimap2.1
@@ -1,4 +1,4 @@
-.TH minimap2 1 "1 July 2017" "minimap2-2.0-r145-pre" "Bioinformatics tools"
+.TH minimap2 1 "5 July 2017" "minimap2-2.0-r158-pre" "Bioinformatics tools"
 .SH NAME
 .PP
 minimap2 - mapping and alignment between collections of DNA sequences
@@ -218,6 +218,9 @@ the final CIGAR. It is the score of the max scoring segment in the alignment
 and may be different from the total alignment score.
 .SS Input/output options
 .TP 10
+.B -Q
+Ignore base quality in the input file.
+.TP
 .B -a
 Generate CIGAR and output alignments in the SAM format. Minimap2 outputs in PAF
 by default.